AFAIK they are automatically shuffled with most-used at the top, so even if you manually rearrange them, they'd eventually be rearranged as visits pile up anyway. But you could certainly edit the visit_counts in .bookmarks/MyBookmarks.xml as a temporary fix.

If you don't know why one would hide some bookmarks in a folder, I bet acou could enlighten you...


EDIT: just realized, if you want to force a fixed ordering, give them, like, 10000, 9000, 8000, etc. visits -- then you'd need 1000 visits to put them out of order. Or do this only for the ones you want at the top, and leave the other ones with genuine numbers so they can be sorted as intended.